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Saffari B, Amininasab M, Sheikhi S, Davoodi J. An efficient method for recombinant production of human alpha synuclein in Escherichia coli using thioredoxin as a fusion partner. Prep Biochem Biotechnol 2020; 50:723-734. [PMID: 32129160 DOI: 10.1080/10826068.2020.1734938] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
Abstract
Herein, we describe a simple and efficient approach to produce recombinant human α-synuclein (hAS) with high purity from Escherichia coli (E. coli). The cDNA for hAS was inserted into plasmid pET32a and expressed in E. coli BL21 (DE3) with an N-terminal tag containing E. coli thioredoxin (trx), followed by a histidine hexapeptide, and a tobacco etch virus (TEV) protease cleavage site (trx-6His-TEV). The fusion protein, trx-hAS, was initially released by osmotic shock treatment from the host cells and subsequently purified using a nickel affinity chromatography. A TEV protease cleavage step was performed to liberate the target protein, hAS, from the fusion partner, trx. Finally, an additional nickel affinity chromatography was performed to further purify the digested product. The yield of this method is ∼25 mg of tag-less protein (with ∼99% purity) per liter of culture volume. Reverse phase HPLC (RP-HPLC) and electrospray ionization (ESI) mass spectrometry confirmed the purity and authenticity of the purified protein. Thioflavin T (ThT) fluorescence assay, transmission electron microscopy (TEM), and circular dichroism (CD) spectroscopy demonstrated that the purified proteins form fibrils. Our protocol not only provides a convenient procedure for preparing highly pure hAS, but also requires very little specialized laboratory techniques.
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Affiliation(s)
- Babak Saffari
- Department of Cell and Molecular Biology, School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - Mehriar Amininasab
- Department of Cell and Molecular Biology, School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - Sara Sheikhi
- Department of Cell and Molecular Biology, School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - Jamshid Davoodi
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
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2
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Hiroaki H, Satomura K, Goda N, Nakakura Y, Hiranuma M, Tenno T, Hamada D, Ikegami T. Spatial Overlap of Claudin- and Phosphatidylinositol Phosphate-Binding Sites on the First PDZ Domain of Zonula Occludens 1 Studied by NMR. Molecules 2018; 23:molecules23102465. [PMID: 30261614 PMCID: PMC6222848 DOI: 10.3390/molecules23102465] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2018] [Revised: 09/20/2018] [Accepted: 09/23/2018] [Indexed: 12/28/2022] Open
Abstract
Background: The tight junction is an intercellular adhesion complex composed of claudins (CLDs), occludin, and the scaffolding proteins zonula occludens 1 (ZO-1) and its two paralogs ZO-2 and ZO-3. ZO-1 is a multifunctional protein that contains three PSD95/Discs large/ZO-1(PDZ) domains. A key functional domain of ZO-1 is the first PDZ domain (ZO-1(PDZ1)) that recognizes the conserved C-termini of CLDs. Methods: In this study, we confirmed that phosphoinositides bound directly to ZO-1(PDZ1) by biochemical and solution NMR experiments. We further determined the solution structure of mouse ZO-1(PDZ1) by NMR and mapped the phosphoinositide binding site onto its molecular surface. Results: The phosphoinositide binding site was spatially overlapped with the CLD-binding site of ZO-1(PDZ1). Accordingly, inositol-hexaphosphate (phytic acid), an analog of the phosphoinositide head group, competed with ZO-1(PDZ)-CLD interaction. Conclusions: The results suggested that the PDZ domain–phosphoinositide interaction plays a regulatory role in biogenesis and homeostasis of the tight junction.
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Affiliation(s)
- Hidekazu Hiroaki
- Laboratory of Structural Molecular Pharmacology, Graduate School of Pharmaceutical Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan.
- Division of Structural Biology, Graduate School of Medicine, Kobe University, Kusunoki-cho, Chuo-ku, Kobe 650-0017, Japan.
- The Structural Biology Research Center and Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan.
| | - Kaori Satomura
- Division of Structural Biology, Graduate School of Medicine, Kobe University, Kusunoki-cho, Chuo-ku, Kobe 650-0017, Japan.
| | - Natsuko Goda
- Laboratory of Structural Molecular Pharmacology, Graduate School of Pharmaceutical Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan.
- Division of Structural Biology, Graduate School of Medicine, Kobe University, Kusunoki-cho, Chuo-ku, Kobe 650-0017, Japan.
| | - Yukako Nakakura
- Laboratory of Structural Molecular Pharmacology, Graduate School of Pharmaceutical Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan.
| | - Minami Hiranuma
- Laboratory of Structural Molecular Pharmacology, Graduate School of Pharmaceutical Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan.
| | - Takeshi Tenno
- Laboratory of Structural Molecular Pharmacology, Graduate School of Pharmaceutical Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan.
- Division of Structural Biology, Graduate School of Medicine, Kobe University, Kusunoki-cho, Chuo-ku, Kobe 650-0017, Japan.
| | - Daizo Hamada
- Division of Structural Biology, Graduate School of Medicine, Kobe University, Kusunoki-cho, Chuo-ku, Kobe 650-0017, Japan.
- Graduate School of Engineering and Center for Applied Structural Science (CASS), Kobe University, Minatojima Minami Machi, Chuo-ku, Kobe 650-0047, Japan.
| | - Takahisa Ikegami
- Institute of Protein Research, Osaka University, Suita, Osaka 565-0871, Japan.
- Structural Epigenetics Laboratory, Graduate School of Medical Life Science, Yokohama-city University, Tsurumi-ku, Yokohama 230-0045 Japan.
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3
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Goda N, Shimizu K, Kuwahara Y, Tenno T, Noguchi T, Ikegami T, Ota M, Hiroaki H. A Method for Systematic Assessment of Intrinsically Disordered Protein Regions by NMR. Int J Mol Sci 2015; 16:15743-60. [PMID: 26184172 PMCID: PMC4519922 DOI: 10.3390/ijms160715743] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Revised: 06/17/2015] [Accepted: 07/01/2015] [Indexed: 11/16/2022] Open
Abstract
Intrinsically disordered proteins (IDPs) that lack stable conformations and are highly flexible have attracted the attention of biologists. Therefore, the development of a systematic method to identify polypeptide regions that are unstructured in solution is important. We have designed an "indirect/reflected" detection system for evaluating the physicochemical properties of IDPs using nuclear magnetic resonance (NMR). This approach employs a "chimeric membrane protein"-based method using the thermostable membrane protein PH0471. This protein contains two domains, a transmembrane helical region and a C-terminal OB (oligonucleotide/oligosaccharide binding)-fold domain (named NfeDC domain), connected by a flexible linker. NMR signals of the OB-fold domain of detergent-solubilized PH0471 are observed because of the flexibility of the linker region. In this study, the linker region was substituted with target IDPs. Fifty-three candidates were selected using the prediction tool POODLE and 35 expression vectors were constructed. Subsequently, we obtained 15N-labeled chimeric PH0471 proteins with 25 IDPs as linkers. The NMR spectra allowed us to classify IDPs into three categories: flexible, moderately flexible, and inflexible. The inflexible IDPs contain membrane-associating or aggregation-prone sequences. This is the first attempt to use an indirect/reflected NMR method to evaluate IDPs and can verify the predictions derived from our computational tools.
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Affiliation(s)
- Natsuko Goda
- Division of Structural Biology, Graduate School of Pharmaceutical Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan.
| | - Kana Shimizu
- Computational Biology Research Center (CBRC), National Institute of Advanced Industrial Science and Technology (AIST), Tokyo Waterfront Bio-IT Research Building 2-4-7 Aomi, Koto-ku, Tokyo 135-0046, Japan.
| | - Yohta Kuwahara
- Division of Structural Biology, Graduate School of Medicine, Kobe University, Kusunoki-cho, 7-5-1, Chuo-ku, Kobe 650-0017, Japan.
| | - Takeshi Tenno
- The Structural Biology Research Center and Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan.
| | - Tamotsu Noguchi
- Pharmaceutical Education Research Center, Meiji Pharmaceutical University, 2-522-1 Noshio, Kiyose, Tokyo 204-8588, Japan.
| | - Takahisa Ikegami
- Institute for Protein Research, Osaka University, Yamadaoka 3-2, Suita, Osaka 565-0871, Japan.
- Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama 230-0045, Japan.
| | - Motonori Ota
- Graduate School of Information Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya 464-8601, Japan.
| | - Hidekazu Hiroaki
- Division of Structural Biology, Graduate School of Pharmaceutical Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan.
- Division of Structural Biology, Graduate School of Medicine, Kobe University, Kusunoki-cho, 7-5-1, Chuo-ku, Kobe 650-0017, Japan.
- The Structural Biology Research Center and Division of Biological Science, Graduate School of Science, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan.
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4
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Goda N, Matsuo N, Tenno T, Ishino S, Ishino Y, Fukuchi S, Ota M, Hiroaki H. An optimized N pro-based method for the expression and purification of intrinsically disordered proteins for an NMR study. INTRINSICALLY DISORDERED PROTEINS 2015; 3:e1011004. [PMID: 28232886 DOI: 10.1080/21690707.2015.1011004] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2014] [Revised: 11/26/2014] [Accepted: 12/01/2014] [Indexed: 02/08/2023]
Abstract
Intrinsically disordered proteins (IDPs) are an emerging concept. IDPs have high flexibility in their polypeptide chains, lacking a stable 3-dimensional structure. Because of the difficulty in performing X-ray crystallography for IDPs, nuclear magnetic resonance (NMR) spectroscopy is the first choice for atomic-level investigation of their nature. Given that isotopically labeled IDP samples are necessary for NMR study, a robust and cost-effective protocol for bacterial expression and purification of IDP is also needed. We employed the Npro (EDDIE)-autoprotease fusion protein system. Although IDPs are believed to be readily degraded by endogenous proteases when expressed in Escherichia coli, Npro-fused IDPs showed excellent resistance to degradation. Seven IDPs of uncharacterized function sampled from the human genome as well as 3 constructs from IDP regions derived from human FancM and Thermococcus kodakarensis Hef were prepared. We improved the protocol of refolding of Npro (EDDIE) to use dialysis, which is convenient for subsequent purification using reversed-phase (RP) HPLC. The method is robust and widely applicable to any IDP sample, promoting the acquisition of experimental data for IDPs in a high-throughput manner.
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Affiliation(s)
- Natsuko Goda
- Laboratory of Structural Molecular Pharmacology; Graduate School of Pharmaceutical Sciences; Nagoya University; Furocho, Chikusa-ku, Nagoya, Japan; These authors equally contributed to the work
| | - Naoki Matsuo
- Laboratory of Structural Molecular Pharmacology; Graduate School of Pharmaceutical Sciences; Nagoya University; Furocho, Chikusa-ku, Nagoya, Japan; These authors equally contributed to the work
| | - Takeshi Tenno
- Laboratory of Structural Molecular Pharmacology; Graduate School of Pharmaceutical Sciences; Nagoya University; Furocho, Chikusa-ku, Nagoya, Japan; The Structural Biology Research Center and Division of Biological Science; Graduate School of Science; Nagoya University; Furocho, Nagoya, Japan
| | - Sonoko Ishino
- Department of Bioscience and Biotechnology; Graduate School of Bioresource and Bioenvironmental Sciences and Faculty of Agriculture; Kyushu University ; Fukuoka, Japan
| | - Yoshizumi Ishino
- Department of Bioscience and Biotechnology; Graduate School of Bioresource and Bioenvironmental Sciences and Faculty of Agriculture; Kyushu University ; Fukuoka, Japan
| | - Satoshi Fukuchi
- Faculty of Engineering, Maebashi Institute of Technology ; Maebashi, Japan
| | - Motonori Ota
- Department of Complex Systems Science; Graduate School of Information Sciences; Nagoya University ; Nagoya, Japan
| | - Hidekazu Hiroaki
- Laboratory of Structural Molecular Pharmacology; Graduate School of Pharmaceutical Sciences; Nagoya University; Furocho, Chikusa-ku, Nagoya, Japan; The Structural Biology Research Center and Division of Biological Science; Graduate School of Science; Nagoya University; Furocho, Nagoya, Japan
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5
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Recombinant expressed vector pET32a (+) S constructed by ligation independent cloning. Molecules 2014; 19:16179-89. [PMID: 25310147 PMCID: PMC6271046 DOI: 10.3390/molecules191016179] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2014] [Revised: 09/09/2014] [Accepted: 09/09/2014] [Indexed: 11/17/2022] Open
Abstract
The aim of this work was to develop a new method for constructing vectors, named ligation-independent cloning (LIC) method. We constructed the S label expression vector and recombinant pET32a (+) S-phoN2 by LIC. The recombinant proteins were expressed in E. coli at a high level, and then the specificity of the recombinant proteins was identified by western blot. The target band was detected by S monoclonal antibody and Apyrase polyclonal antibodies but not Trx monoclonal antibody and HIS monoclonal antibody. Finally, we obtained protein Apyrase in E. coli (BL21), with a protein-only expression S tag. Collectively, our results demonstrated that LIC is effective for the construction of new vectors and recombinant plasmids. Free from the limitations of restriction enzyme sites and with a higher positive rate, LIC processes should find broad applications in molecular biology research.
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6
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Wu R, Wang Q, Zheng Z, Zhao L, Shang Y, Wei X, Liao X, Zhang R. Design, characterization and expression of a novel hybrid peptides melittin (1-13)-LL37 (17-30). Mol Biol Rep 2014; 41:4163-9. [PMID: 24871991 DOI: 10.1007/s11033-013-2900-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Accepted: 12/09/2013] [Indexed: 12/11/2022]
Abstract
Hybridizing of different antimicrobial peptides (AMPs) has been a common practice for obtaining novel hybrid AMPs with elevated antibacterial activity but minimized cytotoxicity. The hybrid peptides melittin (1-13)-LL37 (17-30) (M-L) combining the hydrophobic N-terminal fragment of melittin (M) with the core antibacterial fragment of LL37 (L), was designed for the first time to explore its antibacterial activity and hemolytic activity against bacteria and sheep erythrocyte respectively. Results showed that M-L had an even more potent antibacterial activity against all indicator strains (especially gram-positive bacteria) than M and L, whereas didn't exhibit hemolytic activity to sheep erythrocytes, implying M-L can be served as a potential therapeutic drug to substitute traditional antibiotics. However the high expense of biosynthesis limited its further research, therefore fusion expression of M-L was carried out in Escherichia coli (E. coli) for overproducing the hybrid peptide so as to solve the problem. The DNA sequence encoding M-L with preferred codons was cloned into the pET-SUMO vector for protein expression in E. coli BL21 (DE3). After IPTG induction, approximately 165 mg soluble fusion protein SUMO-M-L was recovered per liter supernatant of the fermentation ultrasonic lysate using Ni-NTA Sepharose column (92 % purity). And 23 mg recombinant M-L was obtained per liter culture after cleavage of SUMO protease and purification of Ni-NTA Sepharose column. In sum, this research not only supplied an effective approach for overproducing hybrid peptide M-L, but paved the way for its further exploration on pharmaceutical potential and medical importance.
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Affiliation(s)
- Rujuan Wu
- Laboratory of Feed Biotechnology, State Key Laboratory of Animal Nutrition, College of Animal Science & Technology, China Agricultural University, No. 2 Yuanmingyuan West Road, Haidian District, Beijing, 100193, People's Republic of China
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7
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Xiao S, Zhao X, Finkielstein CV, Capelluto DGS. A rapid procedure to isolate isotopically labeled peptides for NMR studies: application to the Disabled-2 sulfatide-binding motif. J Pept Sci 2014; 20:216-22. [DOI: 10.1002/psc.2604] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2013] [Revised: 11/17/2013] [Accepted: 11/26/2013] [Indexed: 11/08/2022]
Affiliation(s)
- Shuyan Xiao
- Protein Signaling Domains Laboratory, Department of Biological Sciences, Virginia Bioinformatics Institute; Virginia Tech; Blacksburg VA 24061 USA
| | - Xiaolin Zhao
- Protein Signaling Domains Laboratory, Department of Biological Sciences, Virginia Bioinformatics Institute; Virginia Tech; Blacksburg VA 24061 USA
| | - Carla V. Finkielstein
- Integrated Cellular Responses Laboratory, Department of Biological Sciences, Virginia Bioinformatics Institute; Virginia Tech; Blacksburg VA 24061 USA
| | - Daniel G. S. Capelluto
- Protein Signaling Domains Laboratory, Department of Biological Sciences, Virginia Bioinformatics Institute; Virginia Tech; Blacksburg VA 24061 USA
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8
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Cloning, Expression and Characterization of Sugarcane (Saccharum officinarum L.) Transketolase. Protein J 2013; 32:551-9. [DOI: 10.1007/s10930-013-9516-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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9
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Iwaya N, Takasu H, Goda N, Shirakawa M, Tanaka T, Hamada D, Hiroaki H. MIT domain of Vps4 is a Ca2+-dependent phosphoinositide-binding domain. J Biochem 2013; 153:473-81. [PMID: 23423459 DOI: 10.1093/jb/mvt012] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
The microtubule interacting and trafficking (MIT) domain is a small protein module that is conserved in proteins of diverged function, such as Vps4, spastin and sorting nexin 15 (SNX15). The molecular function of the MIT domain is protein-protein interaction, in which the domain recognizes peptides containing MIT-interacting motifs. Recently, we identified an evolutionarily related domain, 'variant' MIT domain at the N-terminal region of the microtubule severing enzyme katanin p60. We found that the domain was responsible for binding to microtubules and Ca(2+). Here, we have examined whether the authentic MIT domains also bind Ca(2+). We found that the loop between the first and second α-helices of the MIT domain binds a Ca(2+) ion. Furthermore, the MIT domains derived from Vps4b and SNX15a showed phosphoinositide-binding activities in a Ca(2+)-dependent manner. We propose that the MIT domain is a novel membrane-associating domain involved in endosomal trafficking.
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Affiliation(s)
- Naoko Iwaya
- Laboratory of Structural and Molecular Pharmacology, Graduate School of Pharmaceutical Sciences, Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601, Japan
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10
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Umetsu Y, Goda N, Taniguchi R, Satomura K, Ikegami T, Furuse M, Hiroaki H. 1H, 13C, and 15N resonance assignment of the first PDZ domain of mouse ZO-1. BIOMOLECULAR NMR ASSIGNMENTS 2011; 5:207-210. [PMID: 21431884 DOI: 10.1007/s12104-011-9301-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/07/2011] [Accepted: 03/12/2011] [Indexed: 05/30/2023]
Abstract
Zonula occludens-1 (ZO-1) is a scaffolding molecule critical to the formation of intercellular adhesion structures, such as tight junctions (TJs) and adherens junctions (AJs). ZO-1 contains three PDZ domains followed by a GUK domain and a ZU5 domain. The first PDZ of ZO-1 (ZO-1(PDZ1)) serves as a protein-protein interaction module and interacts with the C-termini of almost all claudins to initiate the formation of a belt-like structure on the lateral membranes, thereby promoting TJ formation. It has been recently reported that approximately 15% of all PDZ domains bind phosphoinositides, and ZO-1(PDZ1) is the one of these. Here we report the (15)N, (13)C, and (1)H chemical shift assignments of the first PDZ domain of mouse ZO-1. The resonance assignments obtained in this work may contribute in clarifying the interplay between the two binary interactions, ZO-1(PDZ1)-claudins and ZO-1(PDZ1)-phospholipids, and suggesting a novel regulation mechanism underlying the formation and maintenance of cell-cell adhesion machinery downstream of the phospholipid signaling pathways.
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Affiliation(s)
- Yoshitaka Umetsu
- Division of Structural Biology Graduate School of Medicine, Kobe University, Kobe, Hyogo, Japan
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Fujiwara Y, Fujiwara KI, Goda N, Iwaya N, Tenno T, Shirakawa M, Hiroaki H. Structure and function of the N-terminal nucleolin binding domain of nuclear valosin-containing protein-like 2 (NVL2) harboring a nucleolar localization signal. J Biol Chem 2011; 286:21732-41. [PMID: 21474449 PMCID: PMC3122229 DOI: 10.1074/jbc.m110.174680] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2010] [Revised: 02/28/2011] [Indexed: 11/06/2022] Open
Abstract
The N-terminal regions of AAA-ATPases (ATPase associated with various cellular activities) often contain a domain that defines the distinct functions of the enzymes, such as substrate specificity and subcellular localization. As described herein, we have determined the solution structure of an N-terminal unique domain isolated from nuclear valosin-containing protein (VCP)-like protein 2 (NVL2(UD)). NVL2(UD) contains three α helices with an organization resembling that of a winged helix motif, whereas a pair of β-strands is missing. The structure is unique and distinct from those of other known type II AAA-ATPases, such as VCP. Consequently, we identified nucleolin from a HeLa cell extract as a binding partner of this domain. Nucleolin contains a long (∼300 amino acids) intrinsically unstructured region, followed by the four tandem RNA recognition motifs and the C-terminal glycine/arginine-rich domain. Binding analyses revealed that NVL2(UD) potentially binds to any of the combinations of two successive RNA binding domains in the presence of RNA. Furthermore, NVL2(UD) has a characteristic loop, in which the key basic residues RRKR are exposed to the solvent at the edge of the molecule. The mutation study showed that these residues are necessary and sufficient for nucleolin-RNA complex binding as well as nucleolar localization. Based on the observations presented above, we propose that NVL2 serves as an unfoldase for the nucleolin-RNA complex. As inferred from its RNA dependence and its ATPase activity, NVL2 might facilitate the dissociation and recycling of nucleolin, thereby promoting efficient ribosome biogenesis.
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Affiliation(s)
- Yoshie Fujiwara
- From the Division of Structural Biology, Graduate School of Medicine, and
- the Global Center of Excellence Program for Integrative Membrane Biology, Kobe University, 7-5-1 Kusunokicho, Chuo-ku, Kobe, Hyogo 650-0017, Japan
- the Institute for Bioinformatics Research and Development, Japan Science and Technology Agency, Kawaguchi Center Building, 4-1-8, Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Ken-ichiro Fujiwara
- the Field of Supramolecular Biology, International Graduate School of Arts and Sciences, Yokohama City University, 1-7-29 Suehirocho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
- Shionogi Research Laboratories, Shionogi & Co., Ltd., 5-12-4 Sagisu, Fukushima-ku, Osaka 553-0002, Japan, and
| | - Natsuko Goda
- From the Division of Structural Biology, Graduate School of Medicine, and
- the Institute for Bioinformatics Research and Development, Japan Science and Technology Agency, Kawaguchi Center Building, 4-1-8, Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Naoko Iwaya
- From the Division of Structural Biology, Graduate School of Medicine, and
- the Institute for Bioinformatics Research and Development, Japan Science and Technology Agency, Kawaguchi Center Building, 4-1-8, Honcho, Kawaguchi, Saitama 332-0012, Japan
- the Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-daigaku Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Takeshi Tenno
- From the Division of Structural Biology, Graduate School of Medicine, and
- the Global Center of Excellence Program for Integrative Membrane Biology, Kobe University, 7-5-1 Kusunokicho, Chuo-ku, Kobe, Hyogo 650-0017, Japan
| | - Masahiro Shirakawa
- the Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto-daigaku Katsura, Nishikyo-ku, Kyoto 615-8510, Japan
| | - Hidekazu Hiroaki
- From the Division of Structural Biology, Graduate School of Medicine, and
- the Global Center of Excellence Program for Integrative Membrane Biology, Kobe University, 7-5-1 Kusunokicho, Chuo-ku, Kobe, Hyogo 650-0017, Japan
- the Institute for Bioinformatics Research and Development, Japan Science and Technology Agency, Kawaguchi Center Building, 4-1-8, Honcho, Kawaguchi, Saitama 332-0012, Japan
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12
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Umetsu Y, Tenno T, Goda N, Shirakawa M, Ikegami T, Hiroaki H. Structural difference of vasoactive intestinal peptide in two distinct membrane-mimicking environments. BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS 2011; 1814:724-30. [PMID: 21439408 DOI: 10.1016/j.bbapap.2011.03.009] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/14/2011] [Revised: 03/09/2011] [Accepted: 03/16/2011] [Indexed: 10/18/2022]
Abstract
Vasoactive intestinal peptide (VIP) is a 28-amino acid neuropeptide which belongs to a glucagon/secretin superfamily, the ligand of class II G protein-coupled receptors. Knowledge for the conformation of VIP bound to membrane is important because the receptor activation is initiated by membrane binding of VIP. We have previously observed that VIP-G (glycine-extended VIP) is unstructured in solution, as evidenced by the limited NMR chemical shift dispersion. In this study, we determined the three-dimensional structures of VIP-G in two distinct membrane-mimicking environments. Although these are basically similar structures composed of a disordered N-terminal region and a long α-helix, micelle-bound VIP-G has a curved α-helix. The side chains of residues Phe(6), Tyr(10), Leu(13), and Met(17) found at the concave face form a hydrophobic patch in the micelle-bound state. The structural differences in two distinct membrane-mimicking environments show that the micelle-bound VIP-G localized at the water-micelle boundary with these side chains toward micelle interior. In micelle-bound PACAP-38 (one of the glucagon/secretin superfamily peptide) structure, the identical hydrophobic residues form the micelle-binding interface. This result suggests that these residues play an important role for the membrane binding of VIP and PACAP.
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Affiliation(s)
- Yoshitaka Umetsu
- Graduate School of Medicine, Kobe University, Chuo-ku, Kobe, Hyogo, Japan
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13
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Simeonov P, Berger-Hoffmann R, Hoffmann R, Sträter N, Zuchner T. Surface supercharged human enteropeptidase light chain shows improved solubility and refolding yield. Protein Eng Des Sel 2010; 24:261-8. [PMID: 21084283 DOI: 10.1093/protein/gzq104] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Enteropeptidase is a serine protease used in different biotechnological applications. For many applications the smaller light chain can be used to avoid the expression of the rather large holoenzyme. Recombinant human enteropeptidase light chain (hEPL) shows high activity but low solubility and refolding yields, currently limiting its use in biotechnological applications. Here we describe several protein modifications that lead to improved solubility and refolding yield of human hEPL whilst retaining the enzyme activity. Specifically, protein surface supercharging (N6D, G21D, G22D, N141D, K209E) of the protein increased the solubility more than 100-fold. Replacement of a free cysteine residue with serine (C112S) improved the refolding yield by 50%. The heat stability of this C112S variant was also significantly improved by supercharging. This study shows that even mild protein surface supercharging can have pronounced effects on protein solubility and stability.
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Affiliation(s)
- Peter Simeonov
- Ultrasensitive Protein Detection Unit, Institute of Bioanalytical Chemistry, Center for Biotechnology and Biomedicine, University of Leipzig, Deutscher Platz 5, 04103 Leipzig, Germany
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14
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Hrmova M, Stone BA, Fincher GB. High-yield production, refolding and a molecular modelling of the catalytic module of (1,3)-β-d-glucan (curdlan) synthase from Agrobacterium sp. Glycoconj J 2010; 27:461-76. [DOI: 10.1007/s10719-010-9291-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2009] [Revised: 04/14/2010] [Accepted: 04/14/2010] [Indexed: 11/24/2022]
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15
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Expression of recombinant hybrid peptide hinnavin II/α-melanocyte-stimulating hormone in Escherichia coli: Purification and characterization. J Microbiol 2010; 48:24-9. [DOI: 10.1007/s12275-009-0317-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2009] [Accepted: 02/01/2010] [Indexed: 11/27/2022]
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16
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Hartmann BM, Kaar W, Yoo IK, Lua LHL, Falconer RJ, Middelberg APJ. The chromatography-free release, isolation and purification of recombinant peptide for fibril self-assembly. Biotechnol Bioeng 2009; 104:973-85. [PMID: 19530081 DOI: 10.1002/bit.22447] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
One of the major expenses associated with recombinant peptide production is the use of chromatography in the isolation and purification stages of a bioprocess. Here we report a chromatography-free isolation and purification process for recombinant peptide expressed in Escherichia coli (E. coli). Initial peptide release is by homogenization and then by enzymatic cleavage of the peptide-containing fusion protein, directly in the E. coli homogenate. Release is followed by selective solvent precipitation (SSP) to isolate and purify the peptide away from larger cell contaminants. Specifically, we expressed in E. coli the self-assembling beta-sheet forming peptide P(11)-2 in fusion to thioredoxin. Homogenate was heat treated (55 degrees C, 15 min) and then incubated with tobacco etch virus protease (TEVp) to release P(11)-2 having a native N-terminus. SSP with ethanol at room temperature then removed contaminating proteins in an integrated isolation-purification step; it proved necessary to add 250 mM NaCl to homogenate to prevent P(11)-2 from partitioning to the precipitate. This process structure gave recombinant P(11)-2 peptide at 97% polypeptide purity and 40% overall yield, without a single chromatography step. Following buffer-exchange of the 97% pure product by bind-elute chromatography into defined chemical conditions, the resulting peptide was shown to be functionally active and able to form self-assembled fibrils. To the best of our knowledge, this manuscript reports the first published process for chromatography-free recombinant peptide release, isolation and purification. The process proved able to deliver functional recombinant peptide at high purity and potentially low cost, opening cost-sensitive materials applications for peptide-based materials.
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Affiliation(s)
- B M Hartmann
- Centre for Biomolecular Engineering, Australian Institute for Bioengineering and Nanotechnology, The University of Queensland, St. Lucia, QLD 4072, Australia
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17
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Yanga Y, Tiana Z, Teng D, Zhang J, Wang J, Wang J. High-level production of a candidacidal peptide lactoferrampin in Escherichia coli by fusion expression. J Biotechnol 2009; 139:326-31. [PMID: 19297728 DOI: 10.1016/j.jbiotec.2009.01.003] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Expression of lactoferrampin 265-284 (Lfampin20), a potential candidacidal agent with 20 amino acid segment from lactoferrin, in Escherichia coli was explored. The DNA fragment encoding Lfampin20 was synthesized in light of the E. coli preferred codons by "partially overlapping primer-based PCR" method. The Lfampin20 gene was fused with thioredoxin (Trx) gene to construct a recombinant plasmid pETLfa20. The resulting expression level of the fusion protein Trx-Lfampin20 (approximately 20 kDa) accounted for 34-42% of cellular protein, and about 52% of the target proteins were in a soluble form. Soluble Trx-Lfampin20 accounted for 66% of the total soluble proteins. The soluble fusion protein was easily purified to near homogeneity by affinity chromatography using hexahistidine tag. Recombinant Lfampin20 was effectively obtained by on-column cleavage of the fusion protein with factor Xa. An unknown site in the Trx-tag fusion protein, which can be cleaved by factor Xa to produce approximately 10 kDa protein, was found. Compared with the unknown site, the specific site of IEGR[downwards arrow]X was easier to be recognized and cleaved by factor Xa. The molecular mass of recombinant Lfampin20 determined by MALDI-TOF (matrix assisted laser desorption ionization-time-of-flight) is equal to its theoretical molecular weight. Antimicrobial activity assays demonstrated that the recombinant Lfampin20 had candidacidal activity. Integration of the key strategies for the expression of antimicrobial peptides (AMPs) such as codon usage bias, fusion partner and on-column cleavage, would provide an efficient and facile platform for the production or study of AMPs.
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Affiliation(s)
- Yalin Yanga
- Gene Engineering Laboratory, Feed Research Institute, Chinese Academy of Agricultural Sciences, 12 Zhongguancun Nandajie St., Haidian District, Beijing 100081, PR China
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18
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Biologically active and C-amidated hinnavinII-38-Asn produced from a Trx fusion construct in Escherichia coli. J Microbiol 2008; 46:656-61. [DOI: 10.1007/s12275-008-0214-z] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2008] [Accepted: 10/07/2008] [Indexed: 10/21/2022]
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19
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Komi N, Okawa K, Tateishi Y, Shirakawa M, Fujiwara T, Akutsu H. Structural analysis of pituitary adenylate cyclase-activating polypeptides bound to phospholipid membranes by magic angle spinning solid-state NMR. BIOCHIMICA ET BIOPHYSICA ACTA-BIOMEMBRANES 2007; 1768:3001-11. [PMID: 17996724 DOI: 10.1016/j.bbamem.2007.10.015] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2007] [Revised: 10/06/2007] [Accepted: 10/10/2007] [Indexed: 10/22/2022]
Abstract
PACAP (pituitary adenylate cyclase-activating polypeptide) is a member of the VIP/secretin/glucagon family, which includes the ligands of class II G-protein coupled receptors. Since the recognition of PACAP by the receptor may involve the binding of PACAP to membranes, its membrane-bound structure should be important. We have carried out structural analysis of uniformly 13C,15N labeled PACAP27 and its C-terminal truncated form PACAP(1-21)NH2 (PACAP21) bound to membranes with high resolution solid-state NMR. Phosphatidylcholine bilayers and phosphatidylcholine/phosphatidylglycerol bilayers were used for PACAP27 and PACAP21, respectively. Most backbone signals were assigned for PACAP27 and PACAP21. TALOS analysis revealed that both peptides take on extended conformations on the membranes. Dilution of PACAP21 did not change the conformation of the major part. Selective polarization transfer experiment confirmed that PACAP27 is interacting with the membranes. It was concluded that the interaction of PACAP with the membrane surface causes their extended conformation. PACAP27 is reported to take an alpha-helical conformation in dodecylphosphocholine micelles and membrane-binding peptides usually take similar conformations in micelles and in membranes. Therefore, the property of PACAP27 changing its conformation in response to its environment is unique. Its conformational flexibility may be associated with its wide variety of functions.
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Affiliation(s)
- Nobuyasu Komi
- Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita 565-0871, Japan
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20
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Zhao DX, Ding ZC, Liu YQ, Huang ZX. Overexpression and purification of single zinc finger peptides of human zinc finger protein ZNF191. Protein Expr Purif 2007; 53:232-7. [PMID: 17270462 DOI: 10.1016/j.pep.2006.12.009] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2006] [Revised: 12/11/2006] [Accepted: 12/11/2006] [Indexed: 11/28/2022]
Abstract
ZNF191, a new human zinc finger protein, probably relates to some hereditary diseases and cancers. To obtain structural information of zinc finger domain a convenient method for obtaining milligram quantities of each zinc finger peptide of ZNF191 is necessary. Here, we report an Escherichia coli expression system for rapid and high-level expression of zinc finger 3 and zinc finger 4 of ZNF191. The gene of zinc finger 3 or zinc finger 4 was cloned into pET31b vector to allow expression of single zinc finger peptide as a ketosteroid isomerase (KSI) fusion protein. The KSI-single zinc finger fusion protein was overexpressed in the form of inclusion body, which can be purified by washing several times using buffer solutions, and then be cleaved directly by cyanogen bromide to release single zinc finger peptide. The more than 20mg/L yield of single zinc finger peptide was achieved with more than 95% purity by using YM ultrafiltration membranes. Circular dichroism spectra of these two single zinc finger peptides titrated with Zn(2+) ions demonstrate that they have different secondary structures.
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Affiliation(s)
- Dong-Xin Zhao
- Chemical Biology Lab, Department of Chemistry, Fudan University, Shanghai 200433, PR China
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21
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Xu X, Jin F, Yu X, Ji S, Wang J, Cheng H, Wang C, Zhang W. Expression and purification of a recombinant antibacterial peptide, cecropin, from Escherichia coli. Protein Expr Purif 2007; 53:293-301. [PMID: 17300953 DOI: 10.1016/j.pep.2006.12.020] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2006] [Revised: 12/12/2006] [Accepted: 12/12/2006] [Indexed: 10/23/2022]
Abstract
Insect cecropins are small basic polypeptides synthesized in fat body and hemocytes in response to bacterial infections or hypodermic injuries. To explore a new approach for high expression of soluble cecropin in Escherichia coli cells, we fused the sequence encoding Musca domestica mature cecropin (named Mdmcec) in-frame to thioredoxin (TRX) gene to construct an expression vector pTRX-6His-Mdmcec. An enterokinase cleavage site was introduced between the 6xHis-tag and Mdmcec to facilitate final release of the recombinant Mdmcec. The fusion protein TRX-6His-Mdmcec was purified successfully by HisTrap HP affinity column and a high yield of 48.0mg purified fusion protein was obtained from 1L culture. Recombinant Mdmcec was readily obtained by enterokinase cleavage of the fusion protein followed by HPLC chromatography, and 11.2mg pure active recombinant Mdmcec was obtained from 1L E. coli culture. The molecular mass of recombinant Mdmcec determined by electrospray ionization-mass spectrometry (ESI-MS) is identical to that of native cecropin. Analysis of recombinant Mdmcec by circular dichroism (CD) indicated that recombinant Mdmcec contained predominantly alpha-helix with some random coil. Antimicrobial activity assays demonstrated that recombinant Mdmcec had a broad spectrum of activity against fungi, Gram-positive and negative bacteria. The procedure described in this study will provide a reliable and simple method for production of different cationic peptides for biological studies.
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Affiliation(s)
- Xiaoxia Xu
- State Key Laboratory of Biocontrol, College of Life Sciences, Sun Yat-sen (Zhongshan) University, Guangzhou 510275, PR China
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22
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Goda N, Tenno T, Inomata K, Iwaya N, Sasaki Y, Shirakawa M, Hiroaki H. LBT/PTD dual tagged vector for purification, cellular protein delivery and visualization in living cells. BIOCHIMICA ET BIOPHYSICA ACTA-MOLECULAR CELL RESEARCH 2006; 1773:141-6. [PMID: 17207544 DOI: 10.1016/j.bbamcr.2006.11.016] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2006] [Revised: 11/20/2006] [Accepted: 11/21/2006] [Indexed: 10/23/2022]
Abstract
Cellular protein delivery is an emerging technique, by which exogenous recombinant proteins are delivered into mammalian cells across the membrane. We have developed an E. coli expression vector suited for protein cellular delivery experiments. The plasmid is designed to generate a C-terminal fusion with the 12 amino acid HIV-Tat peptide as a protein transduction domain (PTD), whereas the protein N-terminus is fused to an 17-residue peptide lanthanide-binding tag (LBT). LBT is used for both purification by affinity chromatography and fluorescent detection with Tb(3+) as a coordinating metal. We have employed the TA-cloning site between the two tags, LBT and PTD, according to the PRESAT-vector methodology [N. Goda, T. Tenno, H. Takasu, H. Hiroaki, M. Shirakawa, The PRESAT-vector: asymmetric T-vector for high-throughput screening of soluble protein domains for structural proteomics, Protein Sci. 13 (2004) 652-658], which facilitates unidirectional cloning of any PCR-amplified DNA fragments corresponding to the protein of interest. A simple three-step protocol consisting of affinity purification of LBT/PTD dual-tagged proteins has also been developed, in which the proteins are purified by heparin-, then immobilized Ni(2+)-, and then heparin-affinity chromatography, in this order. The purified protein is ready for protein delivery experiment, and the delivered protein is visible by fluorescent microscopy. Our LBT/PTD dual-tagged PRESAT-vector provides a powerful research tool for exploring cellular functions of proteins in the post-genomic era.
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Affiliation(s)
- Natsuko Goda
- Division of Molecular Biophysics, International Graduate School of Arts and Sciences, Yokohama City University, 1-7-29 Suehiro-cho, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan
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23
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Bao WJ, Gao YG, Chang YG, Zhang TY, Lin XJ, Yan XZ, Hu HY. Highly efficient expression and purification system of small-size protein domains in Escherichia coli for biochemical characterization. Protein Expr Purif 2006; 47:599-606. [PMID: 16427307 DOI: 10.1016/j.pep.2005.11.021] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2005] [Revised: 11/23/2005] [Accepted: 11/25/2005] [Indexed: 11/29/2022]
Abstract
It is often essential to focus the study on the small-size domains of large proteins in eukaryotic cells in the post-genomic era, but the low expression level, insolubility, and instability of the domains have been continuing to hinder the massive purification of domain peptides for structural and biological investigation. In this work, a highly efficient expression and purification system based on a small-size fusion partner GB1 and histidine tag was utilized to solve these problems. Two vectors, namely pGBTNH and pGBH, were constructed to improve expression and facilitate purification. The linker and thrombin cleavage site have been optimized for minimal degradation during purification process. This system has been tested for eight domain peptides varying in size, linker, hydrophobicity, and predicted secondary structure. The results indicate that this system is achievable to produce these domain peptides with high solubility and stability for further biochemical characterization. Moreover, the fusion protein without the linker and thrombin cleavage site is also suitable for spectroscopic studies especially for NMR structural elucidation, if the target peptide is prone to precipitation or easily degraded during purification. This system will be beneficial to the research field of structure and function of small domain and peptide fragment.
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Affiliation(s)
- Wen-Jing Bao
- Key Laboratory of Proteomics, Institute of Biochemistry and Cell Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, China
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